Researchers have found more genes directly linked to cleft lip and cleft palate.
In a new study, a University of Iowa-led research team has identified three genes that when deleted cause cleft lip or palate, a facial deformity that occurs in about 1 in 1,600 babies born in the United States, according to the US Centers for Disease Control and Prevention. Disease control and prevention.
The team identified the genes by performing a high-resolution search across the genomes of more than 1,000 patients with cleft lip/cleft palate, a repository stemming from Iowa’s longstanding involvement in the Worldwide Study of Cleft Lip or Cleft Palate Disorder.
Cleft lip and cleft palate are birth defects that occur when a baby’s lip or mouth does not form properly during pregnancy. On their own, children with cleft lip or cleft palate often have problems feeding and speaking clearly and can get ear infections.
In patients with the disorder, researchers have found small sections of the genome that have been deleted or duplicated, known as copy number variants. In the omitted sections, the researchers looked for genes that were rare even in people with the disorder. This is important because by looking for genetic losses that are rare in people with the disorder—and even rare or nonexistent in anyone else—; It means that these losses must have a central role in the crack, rather than merely contributing to the disturbance.
The researchers then confirmed the genes’ direct association with cleft lip or palate by reducing their function in two species, African clawed frogs and zebrafish. Each of the species developed Notch markers when the function of their target genes decreased.
We have found, and validated in vertebrate experiments, three genes directly associated with this disorder. It will be a long time before we can do anything about it in humans, but now we have added several key genes that drive this disorder. Ultimately, if you know the genes behind cleft lip and cleft palate, and the step-by-step process of how a face is built, you may figure out how to intervene to prevent the defect.”
John Manack, professor in the Iowa State Department of Biology and corresponding author of the study
The causes of orofacial clefts among most children are unknown but are thought to arise from changes in genes and possibly external factors.
The researchers analyzed the DNA of cleft patients in the United States and the Philippines. The broad patient group comes from Jeffrey Murray, MD, professor in the Stead Family Department of Pediatrics at Iowa State. Sandra Duck Hirsch is a professor in the School of Nursing. and many others who have traveled for years to the Philippines to enroll patients with clefts and their family members to collect samples and information about the disorder as part of Operation Smile-sponsored surgical missions.
“The families who generously participated in this study had hoped that this work would one day improve the prevention or treatment of cleft lip/palate, and this work represents a significant step in that direction,” says Murray.
Using the DNA of these patients, Manack used a technique called comparative genomic hybridization to look for deleted fragments of DNA in the group of patients with the disorder compared to a control group that didn’t have cleavage. From there, he sought to find deleted genes that were so rare in the cleft group that less than 1% of the 1,102 patients surveyed had them.
“I wanted to identify the incredibly rare mutations that lead to this disorder, because the mutations that lead to bad things are less frequent in the population,” says Manack, MD, affiliated with the Stead Family Department of Pediatrics and Interdisciplinary Graduate Program in Genetics at Iowa State. . In other words, copy number loss where all you need to do is delete genes, and you get the disorder. This is exciting because it identifies some really key genes in the cleavage pathway. Of course, we also need to check that our candidate genes are actually expressed in the face and it makes sense to participate. In the development of the skull, before we were completely confident in our results.”
The researchers used this analysis to find three genes: COBLL1, RIC1, and ARHGEF38.
When the team reduced the function of these genes in embryos of African frogs and zebrafish, each species showed signs of altered facial development. Experiments with frogs, in particular, were important, as they align more closely with humans in an evolutionary way than with zebrafish, and experiments with frogs produced facial features resembling human slits.
Lisa Lansdon, who received her Ph.D. in genetics from Iowa State in 2018 and is the study’s first author, says research was the primary focus of her thesis. She also supervised a group of undergraduate students who helped conduct the analysis.
says Lansdon, who is currently a clinical assistant professor at the University of Missouri-Kansas City College of Medicine.
The findings build on an earlier study led by Manac, published in 2018, in which he used the same gene-searching techniques in a smaller cohort of people with cleft lip or cleft palate to find one gene directly linked to the disorder, called ISM1. The role of this gene in cleavage has been validated in experiments on clawed frogs, as in this study.
“The real highlight for me was the strategy we used in both studies, to look for rare gene deletions in our disease cohort that were much rarer or absent in our controls,” says Manac. “People generally haven’t thought like that. It’s a lot easier to just sequence genes and then look for more traditional mutations that change gene function.”
He’s also excited that genes are likely to be important in overall facial development.
“There are many pathways, genes, and interactions between many different cell types, so we need to identify all of these components to understand how the face is put together,” Manac says.
The study, “Genome-wide analysis of copy number variation in humans with cleft lip and/or cleft palate, identified COBLL1, RIC1, and ARHGEF38 as cleavage genes.” American Journal of Human Genome.
The study authors from Iowa are Murray, Sidney Arliss, Huan Liu, Armaan Hallas, Alyssa Hahn, Greg Bond, Abby Long, Jennifer Standley, George Wehbe, Duck Hirsch, Benjamin Darbrough, Robert Cornell, and Douglas Houston.
Contributing authors include Amanda Dickinson of Virginia Commonwealth University. Anastasia Tyryshkina and Santhosh Girirajan from Penn State University. Nanette Lee of San Carlos University in the Philippines. and Karen Muhlke of the University of North Carolina.
The National Institutes of Health funded the research.
Lansdon, Los Angeles, et al. (2022) genome-wide analysis of copy number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as cleft genes. American Journal of Human Genome. doi.org/10.1016/j.ajhg.2022.11.012.